{"id":"W4386830032","doi":"10.1101/2023.09.15.557936","title":"High-Throughput Short Sequence Typing Schemes for <i>Pseudomonas aeruginosa</i> and <i>Stenotrophomonas maltophilia</i> pure culture and environmental DNA","year":2023,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Infections and bacterial resistance","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Polytechnique Montréal; Université de Montréal; Institut National de la Recherche Scientifique","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; Aix-Marseille Université; California HIV/AIDS Research Program","keywords":"Stenotrophomonas maltophilia; Biology; Multilocus sequence typing; Typing; Pseudomonas aeruginosa; Computational biology; Genetics; Genotyping; In silico; Microbiology; Genome; Gene; Genotype; Bacteria","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001709575,0.0006806056,0.0007839077,0.001077495,0.0003527795,0.0009467752,0.0007548868,0.0005017732,0.001300787],"category_scores_gemma":[0.002689629,0.0003944418,0.001086183,0.0008562901,0.0003151624,0.0004668098,0.000676603,0.0007167103,0.001843538],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003503342,"about_ca_system_score_gemma":0.0004348744,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0008755566,"about_ca_topic_score_gemma":0.001414442,"domain_scores_codex":[0.9978866,0.0005884361,0.0002308993,0.000442039,0.0006731286,0.000178872],"domain_scores_gemma":[0.9980426,0.0004260997,0.0004740805,0.0004037787,0.0004890403,0.0001644021],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0004666953,0.0001104781,0.00359072,0.0002015386,0.00004741652,0.00009286236,0.0001848914,0.001703406,0.9667659,0.0003450764,0.0005816087,0.02590933],"study_design_scores_gemma":[0.00002304687,0.0005954925,0.007389849,0.00002046411,0.00009640734,0.0002341377,0.00008945564,0.01403721,0.9710838,0.0001619437,0.006212165,0.00005606624],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"methods","genre_scores_codex":[0.6404974,0.0004815955,0.3404081,0.0002617269,0.0001077228,0.001439067,0.008214714,0.006271836,0.002317751],"genre_scores_gemma":[0.5153908,0.0004905931,0.4607671,0.0001317572,0.00004560007,0.001306356,0.01744409,0.0005593033,0.003864341],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.001709575,"threshold_uncertainty_score":0.00904125,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01211741500798266,"score_gpt":0.2194109045843678,"score_spread":0.2072934895763852,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}